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Polymorphism at six microsatellite loci was used to study genetic variability and population structure in six geographically distant natural populations of European hake (Merluccius merluccius L.). Four hundred and eighty‐three individuals were sampled from Trondheimsfjord in Norway, the Celtic Sea, the southern Bay of Biscay, Faro off Portugal, the Mediterranean Sea north of the coast of Tunisia and the Adriatic Sea. Population subdivision was found between Mediterranean and Atlantic samples, θ = 0.029 (P < 0.001). No substructuring was found between samples within the Mediterranean Sea, θ = 0.003 and R_ST = 0.007 (P > 0.05). The Atlantic population structure appears to be more complex than previously suggested by the placement of stock boundaries by the International Council for the Exploration of the Seas (ICES). Analyses based on various models of microsatellite evolution all suggest that …